I've always heard that the rule of thumb is: 3 miles biking = 1 mile running. Obviously this can vary widely depending on intensity, but it's pretty good as a general estimate anyways.

Another poster stated that time and heart rate are a better indicator. This is also true. However, since cycling isn't a weight bearing exercise, if you run and cycle at the same "exertion" level (aka how hard it feels), cycling will usually yield a slightly lower heart rate than running. Meaning you would have to cycle for a longer amount of time to burn the same # of calories.

Of course, all of this is based on hearsay and conjecture, and is therefore probably useless.